/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

#include "itkGDCMImageIO.h"
#include "itkNumericSeriesFileNames.h"
#include "itkImageFileReader.h"
#include "itkImageSeriesWriter.h"
#include "itkMetaDataObject.h"

#include <itkImageRegionIteratorWithIndex.h>
#include <vector>
#include "itksys/SystemTools.hxx"

//  Software Guide : BeginLatex
//
//  This example illustrates how to read a 3D image from a non DICOM file and
//  write it as a series of DICOM slices. with some changed header
//  information. Header
//
//  Please note that modifying the content of a DICOM header is a very risky
//  operation. The Header contains fundamental information about the patient
//  and therefore its consistency must be protected from any data corruption.
//  Before attempting to modify the DICOM headers of your files, you must make
//  sure that you have a very good reason for doing so, and that you can
//  ensure that this information change will not result in a lower quality of
//  health care to be delivered to the patient.
//
//  \index{DICOM!Writing Series}
//
//  Software Guide : EndLatex


int
main(int argc, char * argv[])
{

    if (argc < 3)
    {
        std::cerr << "Usage: " << argv[0];
        std::cerr << " InputImage  OutputDicomDirectory" << std::endl;
        return EXIT_FAILURE;
    }


    using PixelType = signed short;
    constexpr unsigned int Dimension = 3;

    using ImageType = itk::Image<PixelType, Dimension>;
    using ReaderType = itk::ImageFileReader<ImageType>;

    ReaderType::Pointer reader = ReaderType::New();

    reader->SetFileName(argv[1]);

    try
    {
        reader->Update();
    }
    catch (const itk::ExceptionObject & excp)
    {
        std::cerr << "Exception thrown while writing the image" << std::endl;
        std::cerr << excp << std::endl;
        return EXIT_FAILURE;
    }

    using ImageIOType = itk::GDCMImageIO;
    using NamesGeneratorType = itk::NumericSeriesFileNames;

    ImageIOType::Pointer gdcmIO = ImageIOType::New();

    const char * outputDirectory = argv[2];

    itksys::SystemTools::MakeDirectory(outputDirectory);


    using OutputPixelType = signed short;
    constexpr unsigned int OutputDimension = 2;

    using Image2DType = itk::Image<OutputPixelType, OutputDimension>;

    using SeriesWriterType = itk::ImageSeriesWriter<ImageType, Image2DType>;

    NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();

    itk::MetaDataDictionary & dict = gdcmIO->GetMetaDataDictionary();
    std::string               tagkey, value;
    tagkey = "0008|0060"; // Modality
    value = "MR";
    itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
    tagkey = "0008|0008"; // Image Type
    value = "DERIVED\\SECONDARY";
    itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
    tagkey = "0008|0064"; // Conversion Type
    value = "DV";
    itk::EncapsulateMetaData<std::string>(dict, tagkey, value);
    tagkey = "0028|0004"; // Conversion Type
    value = "MONOCHROME2";
    itk::EncapsulateMetaData<std::string>(dict, tagkey, value);


    ImageType::RegionType outputRegion = reader->GetOutput()->GetRequestedRegion();
    ImageType::Pointer outputImage = ImageType::New();
    outputImage->SetRegions(outputRegion);

    std::cout << "Region.Size: " << outputRegion.GetSize() << std::endl;
    const ImageType::SpacingType & spacing = reader->GetOutput()->GetSpacing();
    const ImageType::PointType & inputOrigin = reader->GetOutput()->GetOrigin();
    double                       outputOrigin[Dimension];
    for (unsigned int i = 0; i < Dimension; i++)
    {
        outputOrigin[i] = inputOrigin[i];
    }
    outputImage->SetSpacing(spacing);
    outputImage->SetOrigin(outputOrigin);
    outputImage->Allocate();

    // iterator difine
    using ConstIteratorType = itk::ImageRegionIteratorWithIndex<ImageType>;
    using IteratorType = itk::ImageRegionIteratorWithIndex<ImageType>;

    ConstIteratorType inputIt(reader->GetOutput(), reader->GetOutput()->GetRequestedRegion());
    IteratorType outputIt(outputImage, outputRegion);

    inputIt.GoToBegin();
    outputIt.GoToBegin();

    const ImageType::SizeType &regionSize = outputRegion.GetSize();
    while (!inputIt.IsAtEnd())
    {
        ImageType::IndexType idx = outputIt.GetIndex();
        if (idx[0] == 0 ||  idx[1] == 0 || idx[2] == 0
                || idx[0] == int(regionSize[0]-1)
                || idx[1] == int(regionSize[1]-1)
                || idx[2] == int(regionSize[2]-1)
                ) {
            outputIt.Set(0);

        } else {
            if (inputIt.Get() > 0 ) {
                outputIt.Set(12000);
            } else {
                outputIt.Set(0);
            }
        }
        //std::cout << "idx:" << idx[0] << "," << idx[1] << "," << idx[2] << std::endl;


        ++inputIt;
        ++outputIt;
    }


    SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();

    // seriesWriter->SetInput(reader->GetOutput());
    seriesWriter->SetInput(outputImage);
    seriesWriter->SetImageIO(gdcmIO);


    ImageType::RegionType region =
            reader->GetOutput()->GetLargestPossibleRegion();

    ImageType::IndexType start = region.GetIndex();
    ImageType::SizeType  size = region.GetSize();


    std::string format = outputDirectory;

    format += "/image%03d.dcm";

    namesGenerator->SetSeriesFormat(format.c_str());

    namesGenerator->SetStartIndex(start[2]);
    namesGenerator->SetEndIndex(start[2] + size[2] - 1);
    namesGenerator->SetIncrementIndex(1);


    seriesWriter->SetFileNames(namesGenerator->GetFileNames());


    try
    {
        seriesWriter->Update();
    }
    catch (const itk::ExceptionObject & excp)
    {
        std::cerr << "Exception thrown while writing the series " << std::endl;
        std::cerr << excp << std::endl;
        return EXIT_FAILURE;
    }


    return EXIT_SUCCESS;
}
